关于2019-nCoV, 中国学者已发表了高达50篇期刊文章！
凡是搞计量经济的，都关注这个号了
邮箱：econometrics666@126.com
2019-2020新型冠状病毒性肺炎，始于2019年12月中旬华南海鲜市场里的小摊。中国科学家随后分离出一种新的冠状病毒，命名为2019-nCoV，已发现与SARS-CoV的基因序列至少有70％的相似度。截至2020年1月30日，有近7800多例确诊病例，包括一些医护人员和中国境外的病例。已有170多人死亡，有证据表明人与人之间存在传播风险。
Li, Q., et al. (2020). "Early Transmission Dynamics in Wuhan, China, of Novel Coronavirus–Infected Pneumonia."The New England Journal of Medicine.
BACKGROUND:The initial cases of novel coronavirus (2019-nCoV)–infected pneumonia (NCIP) occurred in Wuhan, Hubei Province, China, in December 2019 and January 2020. We analyzed data on the first 425 confirmed cases in Wuhan to determine the epidemiologic characteristics of NCIP.
METHODS:We collected information on demographic characteristics, exposure history, and illness timelines of laboratory-confirmed cases of NCIP that had been reported by January 22, 2020. We described characteristics of the cases and estimated the key epidemiologic time-delay distributions. In the early period of exponential growth, we estimated the epidemic doubling time and the basic reproductive number.
RESULTS:Among the first 425 patients with confirmed NCIP, the median age was 59 years and 56% were male. The majority of cases (55%) with onset before January 1, 2020, were linked to the Huanan Seafood Wholesale Market, as compared with 8.6% of the subsequent cases. The mean incubation period was 5.2 days (95% confidence interval [CI], 4.1 to 7.0), with the 95th percentile of the distribution at 12.5 days. In its early stages, the epidemic doubled in size every 7.4 days. With a mean serial interval of 7.5 days (95% CI, 5.3 to 19), the basic reproductive number was estimated to be 2.2 (95% CI, 1.4 to 3.9).
CONCLUSIONS:On the basis of this information, there is evidence that human-to-human transmission has occurred among close contacts since the middle of December 2019. Considerable efforts to reduce transmission will be required to control outbreaks if similar dynamics apply elsewhere. Measures to prevent or reduce transmission should be implemented in populations at risk. (Funded by the Ministry of Science and Technology of China and others.)
Chan, J. F.-W., et al. (2020). "A familial cluster of pneumonia associated with the 2019 novel coronavirus indicating person-to-person transmission: a study of a family cluster." The Lancet.
Summary Background An ongoing outbreak of pneumonia associated with a novel coronavirus was reported in Wuhan city, Hubei province, China. Affected patients were geographically linked with a local wet market as a potential source. No data on person-to-person or nosocomial transmission have been published to date. Methods In this study, we report the epidemiological, clinical, laboratory, radiological, and microbiological findings of five patients in a family cluster who presented with unexplained pneumonia after returning to Shenzhen, Guangdong province, China, after a visit to Wuhan, and an additional family member who did not travel to Wuhan. Phylogenetic analysis of genetic sequences from these patients were done. Findings From Jan 10, 2020, we enrolled a family of six patients who travelled to Wuhan from Shenzhen between Dec 29, 2019 and Jan 4, 2020. Of six family members who travelled to Wuhan, five were identified as infected with the novel coronavirus. Additionally, one family member, who did not travel to Wuhan, became infected with the virus after several days of contact with four of the family members. None of the family members had contacts with Wuhan markets or animals, although two had visited a Wuhan hospital. Five family members (aged 36–66 years) presented with fever, upper or lower respiratory tract symptoms, or diarrhoea, or a combination of these 3–6 days after exposure. They presented to our hospital (The University of Hong Kong-Shenzhen Hospital, Shenzhen) 6–10 days after symptom onset. They and one asymptomatic child (aged 10 years) had radiological ground-glass lung opacities. Older patients (aged >60 years) had more systemic symptoms, extensive radiological ground-glass lung changes, lymphopenia, thrombocytopenia, and increased C-reactive protein and lactate dehydrogenase levels. The nasopharyngeal or throat swabs of these six patients were negative for known respiratory microbes by point-of-care multiplex RT-PCR, but five patients (four adults and the child) were RT-PCR positive for genes encoding the internal RNA-dependent RNA polymerase and surface Spike protein of this novel coronavirus, which were confirmed by Sanger sequencing. Phylogenetic analysis of these five patients' RT-PCR amplicons and two full genomes by next-generation sequencing showed that this is a novel coronavirus, which is closest to the bat severe acute respiatory syndrome (SARS)-related coronaviruses found in Chinese horseshoe bats. Interpretation Our findings are consistent with person-to-person transmission of this novel coronavirus in hospital and family settings, and the reports of infected travellers in other geographical regions. Funding The Shaw Foundation Hong Kong, Michael Seak-Kan Tong, Respiratory Viral Research Foundation Limited, Hui Ming, Hui Hoy and Chow Sin Lan Charity Fund Limited, Marina Man-Wai Lee, the Hong Kong Hainan Commercial Association South China Microbiology Research Fund, Sanming Project of Medicine (Shenzhen), and High Level-Hospital Program (Guangdong Health Commission).
Zhu, N., et al. (2020). "A Novel Coronavirus from Patients with Pneumonia in China, 2019." New England Journal of Medicine.
Chen, Y., et al. (2020). "Emerging coronaviruses: genome structure, replication, and pathogenesis." Journal of Medical Virology n/a(n/a).
Abstract The recent emergence of a novel coronavirus (2019-nCoV), which is causing an outbreak of unusual viral pneumonia in patients in Wuhan, a central city in China, is another warning of the risk of coronaviruses posed to public health. In this mini-review, we provide a brief introduction of the general features of coronaviruses and describe diseases caused by different coronaviruses in humans and animals. This review will help understand the biology and potential risk of coronaviruses that exist in richness in wildlife such as bats. This article is protected by copyright. All rights reserved.
Cohen, J. and D. Normile (2020). "New SARS-like virus in China triggers alarm." Science 367(6475): 234.
The discovery that a novel, SARS-like coronavirus explains a cluster of pneumonia cases in Wuhan, China, now allows public health officials worldwide to identify infected people and contain the spread. But the virus, which closely resembles four bat coronaviruses that can infect human cells, has left researchers scrambling to answer many questions. One is the extent of spread, and a case of a Wuhan tourist in Thailand who was detected to have the disease underscores that it has the ability to travel quickly outside of the Chinese megacity. It also remains unclear which animals in the Wuhan seafood market are linked to the outbreak. Although no evidence exists of human-to-human transmission, the Chinese tourist in Thailand and a few of the other infected people in Wuhan say they did not visit the seafood market. Only one of 42 people who have confirmed cases of the disease has died, and he had serious underlying health issues. After criticism surfaced about potential delays in sharing information, Chinese scientists have made six sequences of the virus available, which has allowed other researchers to rapidly develop diagnostic tests and begin synthesizing the virus so it can be studied in animal markets. A major concern is the upcoming Lunar New Year on 25 January, during which hundreds of millions of people travel around the country and could potentially spread the infection.
Dong, N., et al. (2020). "Genomic and protein structure modelling analysis depicts the origin and infectivity of 2019-nCoV, a new coronavirus which caused a pneumonia outbreak in Wuhan, China." bioRxiv: 2020.2001.2020.913368.
Detailed genomic and structure-based analysis of a new coronavirus, namely 2019-nCoV, showed that the new virus is a new type of bat coronavirus and is genetically fairly distant from the human SARS coronavirus. Structure analysis of the spike (S) protein of this new virus showed that its S protein only binds weakly to the ACE2 receptor on human cells whereas the human SARS coronavirus exhibits strongly affinity to the ACE receptor. These findings suggest that the new virus does not readily transmit between humans and should theoretically not able to cause very serious human infection. These data are important to guide design of infection control policy and inform the public on the nature of threat imposed by 2019-nCov when results of direct laboratory tests on this virus are not expected to be available in the near future.
Huang, C., et al. (2020). "Clinical features of patients infected with 2019 novel coronavirus in Wuhan, China." The Lancet.
Summary Background A recent cluster of pneumonia cases in Wuhan, China, was caused by a novel betacoronavirus, the 2019 novel coronavirus (2019-nCoV). We report the epidemiological, clinical, laboratory, and radiological characteristics and treatment and clinical outcomes of these patients. Methods All patients with suspected 2019-nCoV were admitted to a designated hospital in Wuhan. We prospectively collected and analysed data on patients with laboratory-confirmed 2019-nCoV infection by real-time RT-PCR and next-generation sequencing. Data were obtained with standardised data collection forms shared by the International Severe Acute Respiratory and Emerging Infection Consortium from electronic medical records. Researchers also directly communicated with patients or their families to ascertain epidemiological and symptom data. Outcomes were also compared between patients who had been admitted to the intensive care unit (ICU) and those who had not. Findings By Jan 2, 2020, 41 admitted hospital patients had been identified as having laboratory-confirmed 2019-nCoV infection. Most of the infected patients were men (30 [73%] of 41); less than half had underlying diseases (13 [32%]), including diabetes (eight [20%]), hypertension (six [15%]), and cardiovascular disease (six [15%]). Median age was 49·0 years (IQR 41·0–58·0). 27 (66%) of 41 patients had been exposed to Huanan seafood market. One family cluster was found. Common symptoms at onset of illness were fever (40 [98%] of 41 patients), cough (31 [76%]), and myalgia or fatigue (18 [44%]); less common symptoms were sputum production (11 [28%] of 39), headache (three [8%] of 38), haemoptysis (two [5%] of 39), and diarrhoea (one [3%] of 38). Dyspnoea developed in 22 (55%) of 40 patients (median time from illness onset to dyspnoea 8·0 days [IQR 5·0–13·0]). 26 (63%) of 41 patients had lymphopenia. All 41 patients had pneumonia with abnormal findings on chest CT. Complications included acute respiratory distress syndrome (12 [29%]), RNAaemia (six [15%]), acute cardiac injury (five [12%]) and secondary infection (four [10%]). 13 (32%) patients were admitted to an ICU and six (15%) died. Compared with non-ICU patients, ICU patients had higher plasma levels of IL2, IL7, IL10, GSCF, IP10, MCP1, MIP1A, and TNFα. Interpretation The 2019-nCoV infection caused clusters of severe respiratory illness similar to severe acute respiratory syndrome coronavirus and was associated with ICU admission and high mortality. Major gaps in our knowledge of the origin, epidemiology, duration of human transmission, and clinical spectrum of disease need fulfilment by future studies. Funding Ministry of Science and Technology, Chinese Academy of Medical Sciences, National Natural Science Foundation of China, and Beijing Municipal Science and Technology Commission.
The, L. (2020). "Emerging understandings of 2019-nCoV." The Lancet.
“There is an emergency in China, but it has not yet become a global health emergency...WHO is following this outbreak every minute of every day”, said Dr Tedros Ghebreyesus, Director-General of WHO, on Jan 23. A novel coronavirus (2019-nCoV) outbreak is emerging, but it is not yet a Public Health Emergency of International Concern (PHEIC). As we went to press, more than 500 cases have been confirmed in China, as well as in Japan, South Korea, Thailand, and the US. The virus can cause a severe respiratory illness, like SARS and MERS, and human-to-human transmission has been confirmed. These characteristics are driving China's urgent public health actions, as well as international concern. But much remains unknown. The pieces of the puzzle that is 2019-nCoV are only now beginning to come together.
Today, we publish the first clinical data from individuals confirmed to be infected with 2019-nCoV from Wuhan, China. Chaolin Huang and colleagues provide comprehensive findings for the first 41 laboratory-confirmed cases. 27 of these 41 cases had direct exposure to the Wuhan seafood market that is thought to be the initial site of infection from an animal source. All had viral pneumonia. The severity of illness is concerning: almost a third of patients developed acute respiratory distress syndrome requiring intensive care; six patients died; five had acute cardiac injury; and four required ventilation.
Wang, C., et al. (2020). "A novel coronavirus outbreak of global health concern." The Lancet.
In December, 2019, Wuhan, Hubei province, China, became the centre of an outbreak of pneumonia of unknown cause, which raised intense attention not only within China but internationally. Chinese health authorities did an immediate investigation to characterise and control the disease, including isolation of people suspected to have the disease, close monitoring of contacts, epidemiological and clinical data collection from patients, and development of diagnostic and treatment procedures. By Jan 7, 2020, Chinese scientists had isolated a novel coronavirus (CoV) from patients in Wuhan. The genetic sequence of the 2019 novel coronavirus (2019-nCoV) enabled the rapid development of point-of-care real-time RT-PCR diagnostic tests specific for 2019-nCoV (based on full genome sequence data on the Global Initiative on Sharing All Influenza Data [GISAID] platform). Cases of 2019-nCoV are no longer limited to Wuhan. Nine exported cases of 2019-nCoV infection have been reported in Thailand, Japan, Korea, the USA, Vietnam, and Singapore to date, and further dissemination through air travel is likely.
As of Jan 23, 2020, confirmed cases were consecutively reported in 32 provinces, municipalities, and special administrative regions in China, including Hong Kong, Macau, and Taiwan.These cases detected outside Wuhan, together with the detection of infection in at least one household cluster—reported by Jasper Fuk-Woo Chan and colleagues in The Lancet—and the recently documented infections in health-care workers caring for patients with 2019-nCoV indicate human-to-human transmission and thus the risk of much wider spread of the disease. As of Jan 23, 2020, a total of 835 cases with laboratory-confirmed 2019-nCoV infection have been detected in China, of whom 25 have died and 93% remain in hospital.
China responded quickly by informing the World Health Organization (WHO) of the outbreak and sharing sequence information with the international community after discovery of the causative agent. The WHO responded rapidly by coordinating diagnostics development; issuing guidance on patient monitoring, specimen collection, and treatment; and providing up-to-date information on the outbreak.3 Several countries in the region as well as the United States are screening travelers from Wuhan for fever, aiming to detect 2019-nCoV cases before the virus spreads further. Updates from China, Thailand, Korea, and Japan indicate that the disease associated with 2019-nCoV appears to be relatively mild as compared with SARS and MERS.
Ji, W., et al. (2020). "Homologous recombination within the spike glycoprotein of the newly identified coronavirus may boost cross-species transmission from snake to human." Journal of Medical Virology n/a(n/a).
Abstract The current outbreak of viral pneumonia in the city of Wuhan, China, was caused by a novel coronavirus designated 2019-nCoV by the World Health Organization, as determined by sequencing the viral RNA genome. Many patients were potentially exposed to wildlife animals at the Huanan seafood wholesale market, where poultry, snake, bats, and other farm animals were also sold. To determine the possible virus reservoir, we have carried out comprehensive sequence analysis and comparison in conjunction with relative synonymous codon usage (RSCU) bias among different animal species based on existing sequences of the newly identified coronavirus 2019-nCoV. Results obtained from our analyses suggest that the 2019-nCoV appears to be a recombinant virus between the bat coronavirus and an origin-unknown coronavirus. The recombination occurred within the viral spike glycoprotein, which recognizes cell surface receptor. Additionally, our findings suggest that snake is the most probable wildlife animal reservoir for the 2019-nCoV based on its RSCU bias resembling snake compared to other animals. Taken together, our results suggest that homologous recombination within the spike glycoprotein may contribute to cross-species transmission from snake to humans. This article is protected by copyright. All rights reserved.
Ji, W., et al. (2020). "Homologous recombination within the spike glycoprotein of the newly identified coronavirus may boost cross-species transmission from snake to human." Journal of Medical Virology n/a(n/a).
Abstract The current outbreak of viral pneumonia in the city of Wuhan, China, was caused by a novel coronavirus designated 2019-nCoV by the World Health Organization, as determined by sequencing the viral RNA genome. Many patients were potentially exposed to wildlife animals at the Huanan seafood wholesale market, where poultry, snake, bats, and other farm animals were also sold. To determine the possible virus reservoir, we have carried out comprehensive sequence analysis and comparison in conjunction with relative synonymous codon usage (RSCU) bias among different animal species based on existing sequences of the newly identified coronavirus 2019-nCoV. Results obtained from our analyses suggest that the 2019-nCoV appears to be a recombinant virus between the bat coronavirus and an origin-unknown coronavirus. The recombination occurred within the viral spike glycoprotein, which recognizes cell surface receptor. Additionally, our findings suggest that snake is the most probable wildlife animal reservoir for the 2019-nCoV based on its RSCU bias resembling snake compared to other animals. Taken together, our results suggest that homologous recombination within the spike glycoprotein may contribute to cross-species transmission from snake to humans. This article is protected by copyright. All rights reserved.
Letko, M. and V. Munster (2020). "Functional assessment of cell entry and receptor usage for lineage B β-coronaviruses, including 2019-nCoV." bioRxiv: 2020.2001.2022.915660.
Over the past 20 years, several coronaviruses have crossed the species barrier into humans, causing outbreaks of severe, and often fatal, respiratory illness. Since SARS- CoV was first identified in animal markets, global viromics projects have discovered thousands of coronavirus sequences in diverse animals and geographic regions. Unfortunately, there are few tools available to functionally test these novel viruses for their ability to infect humans, which has severely hampered efforts to predict the next zoonotic viral outbreak. Here we developed an approach to rapidly screen lineage B betacoronaviruses, such as SARS-CoV and the recent 2019-nCoV, for receptor usage and their ability to infect cell types from different species. We show that host protease processing during viral entry is a significant barrier for several lineage B viruses and that bypassing this barrier allows several lineage B viruses to enter human cells through an unknown receptor. We also demonstrate how different lineage B viruses can recombine to gain entry into human cells and confirm that human ACE2 is the receptor for the recently emerging 2019-nCoV.
Li, G., et al. (2020). "Coronavirus Infections and Immune Responses." Journal of Medical Virology n/a(n/a).
Abstract Coronaviruses (CoVs) are by far the largest group of known positive-sense RNA viruses having an extensive range of natural hosts. In the past few decades, newly evolved Coronaviruses have posed a global threat to public health. Immune response is essential to control and eliminate CoV infections, however, maladjusted immune responses may result in immunopathology and impaired pulmonary gas exchange. Gaining a deeper understanding of the interaction between Coronaviruses and the innate immune systems of the hosts may shed light on the development and persistence of inflammation in the lungs and hopefully can reduce the risk of lung inflammation caused by CoVs. In this review, we provide an update on CoV infections and relevant diseases, particularly the host defense against CoV-induced inflammation of lung tissue, as well as the role of the innate immune system in pathogenesis and clinical treatment. This article is protected by copyright. All rights reserved.
Liu, S.-L. and L. Saif (2020). "Emerging Viruses without Borders: The Wuhan Coronavirus." Viruses 12(2).
The recently emerged coronavirus in Wuhan, China has claimed at least 6 lives as of January 22 and infected hundreds if not thousands of individuals. The situation has drawn international attention, including from the virology community. We applaud the rapid release to the public of the genome sequence of the new virus by Chinese virologists, but we also believe that increased transparency on disease reporting and data sharing with international colleagues are crucial for curbing the spread of this newly emerging virus to other parts of the world.
Luo, G. and S.-J. Gao (2020). "Global Health Concern Stirred by Emerging Viral Infections." Journal of Medical Virology n/a(n/a).
Abstract Emerging viral infections continue to pose a major threat to global public health. In 1997, a highly pathogenic avian influenza A (H5N1) virus was found to directly spread from poultry to humans unlike previously reported transmission routs of human-to-human and livestock-to-human, stirring a grave concern for a possible influenza pandemic. This article is protected by copyright. All rights reserved.
Mahase, E. (2020). "China coronavirus: what do we know so far?" BMJ 368: m308.
Since reports of a mysterious pneumonia-like condition began circulating in December, the public health world has been keeping its eye on the events unfolding in China.1 As the numbers of confirmed cases and deaths have risen, details of the novel coronavirus now known as 2019-nCoV have dripped through. Here’s what we know so far about this evolving situation.The initial source of 2019-nCoV is still unknown, but the first cases were linked to a seafood market in the city of Wuhan, capital of the central Hubei province. The market was closed on 1 January 2020 as part of efforts to contain the outbreak.2As at 24 January 830 cases and 26 deaths had been confirmed worldwide.3 Of the confirmed cases, around 25% are thought to be severe. Outside mainland China cases have been confirmed in Thailand, Japan, Hong Kong, Taiwan, South Korea, and the US. Cases had been reported in the UK but not yet confirmed.The MRC Centre for Global Infectious Disease Analysis at Imperial College London has estimated that by 18 January 4000 people in Wuhan should have shown symptoms caused by the novel disease (uncertainty …
Majumder, M. and K. D. Mandl (2020). "Early Transmissibility Assessment of a Novel Coronavirus in Wuhan, China ".
Between December 1, 2019 and January 26, 2020, nearly 3000 cases of respiratory illness caused by a novel coronavirus originating in Wuhan, China have been reported. In this short analysis, we combine publicly available cumulative case data from the ongoing outbreak with phenomenological modeling methods to conduct an early transmissibility assessment. Our model suggests that the basic reproduction number associated with the outbreak (at time of writing) may range from 2.0 to 3.1. Though these estimates are preliminary and subject to change, they are consistent with previous findings regarding the transmissibility of the related SARS-Coronavirus and indicate the possibility of epidemic potential.
Nishiura, H., et al. (2020). "The Extent of Transmission of Novel Coronavirus in Wuhan, China, 2020." Journal of Clinical Medicine 9(2).
A cluster of pneumonia cases linked to a novel coronavirus (2019-nCoV) was reported by China in late December 2019. Reported case incidence has now reached the hundreds, but this is likely an underestimate. As of 24 January 2020, with reports of thirteen exportation events, we estimate the cumulative incidence in China at 5502 cases (95% confidence interval: 3027, 9057). The most plausible number of infections is in the order of thousands, rather than hundreds, and there is a strong indication that untraced exposures other than the one in the epidemiologically linked seafood market in Wuhan have occurred.
Paraskevis, D., et al. (2020). "Full-genome evolutionary analysis of the novel corona virus (2019-nCoV) rejects the hypothesis of emergence as a result of a recent recombination event." Infection, Genetics and Evolution: 104212.
Background A novel coronavirus (2019-nCoV) associated with human to human transmission and severe human infection has been recently reported from the city of Wuhan in China. Our objectives were to characterize the genetic relationships of the 2019-nCoV and to search for putative recombination within the subgenus of sarbecovirus. Methods Putative recombination was investigated by RDP4 and Simplot v3.5.1 and discordant phylogenetic clustering in individual genomic fragments was confirmed by phylogenetic analysis using maximum likelihood and Bayesian methods. Results Our analysis suggests that the 2019-nCoV although closely related to BatCoV RaTG13 sequence throughout the genome (sequence similarity 96.3%), shows discordant clustering with the Bat_SARS-like coronavirus sequences. Specifically, in the 5′-part spanning the first 11,498 nucleotides and the last 3′-part spanning 24,341–30,696 positions, 2019-nCoV and RaTG13 formed a single cluster with Bat_SARS-like coronavirus sequences, whereas in the middle region spanning the 3′-end of ORF1a, the ORF1b and almost half of the spike regions, 2019-nCoV and RaTG13 grouped in a separate distant lineage within the sarbecovirus branch. Conclusions The levels of genetic similarity between the 2019-nCoV and RaTG13 suggest that the latter does not provide the exact variant that caused the outbreak in humans, but the hypothesis that 2019-nCoV has originated from bats is very likely. We show evidence that the novel coronavirus (2019-nCov) is not-mosaic consisting in almost half of its genome of a distinct lineage within the betacoronavirus. These genomic features and their potential association with virus characteristics and virulence in humans need further attention.
Parry, J. (2020). "Pneumonia in China: lack of information raises concerns among Hong Kong health workers." BMJ 368: m56.
An outbreak of pneumonia of unknown cause in Wuhan, China, has prompted authorities in neighbouring Hong Kong, Macau, and Taiwan to step up border surveillance, amid fears that it could signal the emergence of a new and serious threat to public health.On 5 January local, provincial, and national health commissions reported a cluster of 59 reported cases centred around the South China Seafood Wholesale Market in Wuhan, a city of 11 million people and the capital of Hubei province. They had already ruled out known influenza viruses and the two coronaviruses known to cause severe acute respiratory illness (SARS) and Middle East respiratory syndrome.The limited information that has been released by mainland Chinese authorities is causing unease among the general population and healthcare workers in Hong Kong. The city has a strong collective memory of the SARS outbreak in 2003, which …
Read, J. M., et al. (2020). "Novel coronavirus 2019-nCoV: early estimation of epidemiological parameters and epidemic predictions." medRxiv: 2020.2001.2023.20018549.
Since first identified, the epidemic scale of the recently emerged novel coronavirus (2019-nCoV) in Wuhan, China, has increased rapidly, with cases arising across China and other countries and regions. using a transmission model, we estimate a basic reproductive number of 3.11 (95%CI, 2.39-4.13); 58-76% of transmissions must be prevented to stop increasing; Wuhan case ascertainment of 5.0% (3.6-7.4); 21022 (11090-33490) total infections in Wuhan 1 to 22 January.Competing Interest StatementThe authors have declared no competing interest.Funding StatementJMR and CPJ acknowledge support from the Medical Research Council (MR/5004793/1). JMR acknowledges support from the Engineering and Physical Sciences Research Council (EP/N014499/1). JREB acknowledges support from Faculty of Health and Medicine, Lancaster University in the form of a PhD Scholarship. CPJ acknowledges support from Wellcome.Author DeclarationsAll relevant ethical guidelines have been followed; any necessary IRB and/or ethics committee approvals have been obtained and details of the IRB/oversight body are included in the manuscript.YesAll necessary patient/participant consent has been obtained and the appropriate institutional forms have been archived.YesI understand that all clinical trials and any other prospective interventional studies must be registered with an ICMJE-approved registry, such as ClinicalTrials.gov. I confirm that any such study reported in the manuscript has been registered and the trial registration ID is provided (note: if posting a prospective study registered retrospectively, please provide a statement in the trial ID field explaining why the study was not registered in advance).Yes I have followed all appropriate research reporting guidelines and uploaded the relevant EQUATOR Network research reporting checklist(s) and other pertinent material as supplementary files, if applicable.YesThe collated case and population data used for modelling is provided at a linked repository. Domestic and international airline passenger data are available via subscription from OAG (www.oag.com).https://github.com/chrism0dwk/wuhan/tree/v0.2
Riou, J. and C. L. Althaus (2020). "Pattern of early human-to-human transmission of Wuhan 2019-nCoV." bioRxiv: 2020.2001.2023.917351.
On December 31, 2019, the World Health Organization was notified about a cluster of pneumonia of unknown aetiology in the city of Wuhan, China. Chinese authorities later identified a new coronavirus (2019-nCoV) as the causative agent of the outbreak. As of January 23, 2020, 655 cases have been confirmed in China and several other countries. Understanding the transmission characteristics and the potential for sustained human-to-human transmission of 2019-nCoV is critically important for coordinating current screening and containment strategies, and determining whether the outbreak constitutes a public health emergency of international concern (PHEIC). We performed stochastic simulations of early outbreak trajectories that are consistent with the epidemiological findings to date. We found the basic reproduction number, R0, to be around 2.2 (90% high density interval 1.4—3.8), indicating the potential for sustained human-to-human transmission. Transmission characteristics appear to be of a similar magnitude to severe acute respiratory syndrome-related coronavirus (SARS-CoV) and the 1918 pandemic influenza. These findings underline the importance of heightened screening, surveillance and control efforts, particularly at airports and other travel hubs, in order to prevent further international spread of 2019-nCoV.
Zhao, S., et al. (2020). "Preliminary estimation of the basic reproduction number of novel coronavirus (2019-nCoV) in China, from 2019 to 2020: A data-driven analysis in the early phase of the outbreak." bioRxiv: 2020.2001.2023.916395.
Backgrounds There has been a novel coronavirus (2019-nCoV) pneumonia outbreak in China since December 2019, and which spreads internationally. This is the first study to quantify the basic reproduction number, R0, of 2019-nCoV in the early phase of the outbreak.Methods Accounting for the impact of the variations in disease reporting rate, we modelled the epidemic curve of 2019-nCoV cases time series, in mainland China from January 10 to January 21, 2020, through the exponential growth. With the estimated intrinsic growth rate (γ), we estimated R0 by using the serial intervals (SI) of two other well-known coronavirus diseases, MERS and SARS, as approximations for the true unknown SI.Findings The early outbreak data largely follows the exponential growth. We estimated that the mean R0 ranges from 3.30 (95%CI: 2.73-3.96) to 5.47 (95%CI: 4.16-7.10) associated with 0-fold to 2-fold increase in the reporting rate. With rising report rate, the mean R0 is likely to be below 5 but above 3.Conclusion The mean estimate of R0 for the 2019-nCoV ranges from 3.30 (95%CI: 2.73-3.96) to 5.47 (95%CI: 4.16-7.10), and significantly larger than 1. Our findings indicate the potential of 2019-nCoV to cause outbreaks.
Zhou, P., et al. (2020). "Discovery of a novel coronavirus associated with the recent pneumonia outbreak in humans and its potential bat origin." bioRxiv: 2020.2001.2022.914952.
Since the SARS outbreak 18 years ago, a large number of severe acute respiratory syndrome related coronaviruses (SARSr-CoV) have been discovered in their natural reservoir host, bats. Previous studies indicated that some of those bat SARSr-CoVs have the potential to infect humans. Here we report the identification and characterization of a novel coronavirus (nCoV-2019) which caused an epidemic of acute respiratory syndrome in humans, in Wuhan, China. The epidemic, started from December 12th, 2019, has caused 198 laboratory confirmed infections with three fatal cases by January 20th, 2020. Full-length genome sequences were obtained from five patients at the early stage of the outbreak. They are almost identical to each other and share 79.5% sequence identify to SARS-CoV. Furthermore, it was found that nCoV-2019 is 96% identical at the whole genome level to a bat coronavirus. The pairwise protein sequence analysis of seven conserved non-structural proteins show that this virus belongs to the species of SARSr-CoV. The nCoV-2019 virus was then isolated from the bronchoalveolar lavage fluid of a critically ill patient, which can be neutralized by sera from several patients. Importantly, we have confirmed that this novel CoV uses the same cell entry receptor, ACE2, as SARS-CoV.
Zhu, H., et al. (2020). "Host and infectivity prediction of Wuhan 2019 novel coronavirus using deep learning algorithm." bioRxiv: 2020.2001.2021.914044.
The recent outbreak of pneumonia in Wuhan, China caused by the 2019 Novel Coronavirus (2019-nCoV) emphasizes the importance of detecting novel viruses and predicting their risks of infecting people. In this report, we introduced the VHP (Virus Host Prediction) to predict the potential hosts of viruses using deep learning algorithm. Our prediction suggests that 2019-nCoV has close infectivity with other human coronaviruses, especially the severe acute respiratory syndrome coronavirus (SARS-CoV), Bat SARS-like Coronaviruses and the Middle East respiratory syndrome coronavirus (MERS-CoV). Based on our prediction, compared to the Coronaviruses infecting other vertebrates, bat coronaviruses are assigned with more similar infectivity patterns with 2019-nCoVs. Furthermore, by comparing the infectivity patterns of all viruses hosted on vertebrates, we found mink viruses show a closer infectivity pattern to 2019-nCov. These consequences of infectivity pattern analysis illustrate that bat and mink may be two candidate reservoirs of 2019-nCov.These results warn us to beware of 2019-nCoV and guide us to further explore the properties and reservoir of it.
Benvenuto, D., et al. (2020). "The 2019-new coronavirus epidemic: evidence for virus evolution." bioRxiv: 2020.2001.2024.915157.
There is concern about a new coronavirus, the 2019-nCoV, as a global public health threat. In this article, we provide a preliminary evolutionary and molecular epidemiological analysis of this new virus. A phylogenetic tree has been built using the 15 available whole genome sequence of 2019-nCoV and 12 whole genome sequences highly similar sequences available in gene bank (5 from SARS, 2 from MERS and 5 from Bat SARS-like Coronavirus). FUBAR analysis shows that the Nucleocapsid and the Spike Glycoprotein has some sites under positive pressure while homology modelling helped to explain some molecular and structural differences between the viruses. The phylogenetic tree showed that 2019.nCoV significantly clustered with Bat SARS-like Coronavirus sequence isolated in 2015, whereas structural analysis revealed mutation in S and nucleocapsid proteins. From these results, 2019nCoV could be considered a coronavirus distinct from SARS virus, probably transmitted from bats or another host where mutations conferred upon it the ability to infect humans.
Bagcchi, S. (2020). "Mysterious pneumonia in China." The Lancet Infectious Diseases 20(2): 173.
Biscayart, C., et al. (2020). "The next big threat to global health? 2019 novel coronavirus (2019-nCoV): What advice can we give to travellers? – Interim recommendations January 2020, from the Latin-American society for Travel Medicine (SLAMVI)." Travel Medicine and Infectious Disease: 101567.
Bonilla-Aldana, D. K., et al. (2020). "SARS-CoV, MERS-CoV and now the 2019-novel CoV: Have we investigated enough about coronaviruses? – A bibliometric analysis." Travel Medicine and Infectious Disease: 101566.
Gralinski, L. E. and V. D. Menachery (2020). "Return of the Coronavirus: 2019-nCoV." 12(2): 135.
Hamzelou, J. (2020). "Chinese illness caused by a virus." New Scientist 245(3265): 5.
MacIntyre, C. R. (2020). "Wuhan novel coronavirus 2019nCoV." Global Biosecurity 1(3).
Hamzelou, J. (2020). "Wuhan virus spreads." New Scientist 245(3266): 7.
We now know the virus responsible for deaths and infections in China can pass between people, reports Jessica Hamzelou
Shao, Y. and J. Wu (2020). "IDM editorial statement on the 2019-nCoV." Infectious Disease Modelling 5: 233-234.
Tang, J. W., et al. (2020). "Emergence of a novel coronavirus causing respiratory illness from Wuhan, China." Journal of Infection.
team, E. e. (2020). "Note from the editors: novel coronavirus (2019-nCoV)." 25(3): 2001231.
Wang, R., et al. (2020). "Emergence of SARS-like Coronavirus poses new challenge in China." Journal of Infection.
Wu, P., et al. (2020). "Real-time tentative assessment of the epidemiological characteristics of novel coronavirus infections in Wuhan, China, as at 22 January 2020." 25(3): 2000044.
下面这些短链接文章属于合集，可以收藏起来阅读，不然以后都找不到了。
2年，计量经济圈公众号近1000篇文章，
Econometrics Circle
数据系列：空间矩阵 | 工企数据 | PM2.5 | 市场化指数 | CO2数据 | 夜间灯光 | 官员方言 | 微观数据 |
计量系列：匹配方法 | 内生性 | 工具变量 | DID | 面板数据 | 常用TOOL | 中介调节 | 时间序列 | RDD断点 | 合成控制 |
数据处理：Stata | R | Python | 缺失值 | CHIP/ CHNS/CHARLS/CFPS/CGSS等 |
干货系列：能源环境 | 效率研究 | 空间计量 | 国际经贸 | 计量软件 | 商科研究 | 机器学习 | SSCI | CSSCI | SSCI查询 |
计量经济圈组织了一个计量社群，有如下特征：热情互助最多、前沿趋势最多、社科资料最多、社科数据最多、科研牛人最多、海外名校最多。因此，建议积极进取和有强烈研习激情的中青年学者到社群交流探讨，始终坚信优秀是通过感染优秀而互相成就彼此的。